Question

Slow Download From TCGA

1

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9.4 years ago

dirigible2012 ▴ 320

Is anybody else having problems with a slow download of files from TCGA? At the moment it's taking me 1 hour to download 1 Gb of data using the File Search. My downloads of files from other sources run at about 5MB/second.

Is there anything I can do about this?

Thanks,

Stephanie

TCGA • 2.9k views

ADD COMMENT • link 9.4 years ago by dirigible2012 ▴ 320

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Suddenly, Biostars feels like a homey bioinformatics lab, where everyone pings each other over IM when the cluster disks are being slow. :)

ADD REPLY • link 9.4 years ago by Cyriac Kandoth 6.0k

score 2 · Answer 1 · 2014-11-20

I'm getting decent speeds of 4.7 to 5 MB/s, or roughly 40 Mb/s, from the TCGA DCC housed in Bethesda MD, while I'm located relatively nearby in New York. Instead of using File Search, have you tried downloading data directly from the public https share? For example, to download the clinical data matrix for TCGA BRCA, you could do something like:

curl -LO https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/luad/bcr/biotab/clin/nationwidechildrens.org_clinical_patient_luad.txt

If you have credentials to access data in the protected https share, then you can use wget with --user specified, and --ask-password so that it prompts you for one.